Complete Sequence of pABTJ2, A Plasmid from Acinetobacter baumannii MDR-TJ, Carrying Many Phage-like Elements

Genomics, Proteomics and Bioinformatics

Volumn 12, Issue 4, 2014, Pages 172-177

  Huang, He ^a   Dong, Yan ^a   Yang, Zhi Liang ^a   Luo, Hao ^a   Zhang, Xi ^a   Gao, Feng ^a,b  

^a TIANJIN UNIVERSITY   (China)

^b SynBio Research Platform   (China)

Author keywords

A. baumannii; Phage like elements; Plasmid; tRNA gene

Indexed keywords

ASPARAGINE; CIRCULAR DNA; DOUBLE STRANDED DNA; TRANSFER RNA; BACTERIAL DNA;

ACINETOBACTER BAUMANNII; ACINETOBACTER BAUMANNII MDR-TJ; BACTERIAL CHROMOSOME; BACTERIAL GENE; BACTERIAL GENOME; BACTERIOPHAGE; BACTERIUM ISOLATE; CODON; DNA BASE COMPOSITION; DNA REPLICATION ORIGIN; GENE MAPPING; GENETIC ANALYSIS; GENETIC CODE; LETTER; MULTIDRUG RESISTANCE; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMID; PLASMID ABTJ2; STRUCTURAL GENE; A. BAUMANNII; ACINETOBACTER INFECTION; CLASSIFICATION; GENETICS; HUMAN; ISOLATION AND PURIFICATION; MICROBIOLOGY; PHAGE-LIKE ELEMENTS; PHYLOGENY; SINGLE NUCLEOTIDE POLYMORPHISM; TRNA GENE;

ACINETOBACTER BAUMANNII;

A. BAUMANNII; PHAGE-LIKE ELEMENTS; PLASMID; TRNA GENE;

ACINETOBACTER BAUMANNII; ACINETOBACTER INFECTIONS; BACTERIOPHAGES; DNA, BACTERIAL; HUMANS; PHYLOGENY; PLASMIDS; POLYMORPHISM, SINGLE NUCLEOTIDE; RNA, TRANSFER;

EID: 84909635364     PISSN: 16720229     EISSN: 22103244     Source Type: Journal    
DOI: 10.1016/j.gpb.2014.05.001     Document Type: Letter

References (27)

1. Peleg A.Y., Seifert H., Paterson D.L. Acinetobacter baumannii: emergence of a successful pathogen. Clin Microbiol Rev 2008, 21:538-582.
2. García-Quintanilla M., Pulido M.R., López-Rojas R., Pachón J., McConnell M.J. Emerging therapies for multidrug resistant Acinetobacter baumannii. Trends Microbiol 2013, 21:157-163.
3. Bertini A., Poirel L., Mugnier P.D., Villa L., Nordmann P., Carattoli A. Characterization and PCR-based replicon typing of resistance plasmids in Acinetobacter baumannii. Antimicrob Agents Chemother 2010, 54:4168-4177.
4. Poirel L., Nordmann P. Carbapenem resistance in Acinetobacter baumannii: mechanisms and epidemiology. Clin Microbiol Infect 2006, 12:826-836.
5. Fondi M., Bacci G., Brilli M., Papaleo M.C., Mengoni A., Vaneechoutte M., et al. Exploring the evolutionary dynamics of plasmids: the Acinetobacter pan-plasmidome. BMC Evol Biol 2010, 10:59.
6. Carattoli A. Plasmids and the spread of resistance. Int J Med Microbiol 2013, 303:298-304.
7. Huang H., Yang Z.L., Wu X.M., Wang Y., Liu Y.J., Luo H., et al. Complete genome sequence of Acinetobacter baumannii MDR-TJ and insights into its mechanism of antibiotic resistance. J Antimicrob Chemother 2012, 67:2825-2832.
8. Wajid B., Serpedin E. Review of general algorithmic features for genome assemblers for next generation sequencers. Genomics Proteomics Bioinformatics 2012, 10:58-73.
9. Jiang S.C., Paul J.H. Significance of lysogeny in the marine environment studies with isolates and a model of lysogenic phage production. Microb Ecol 1998, 35:235-243.
10. Chattoraj D.K. Control of plasmid DNA replication by iterons: no longer paradoxical. Mol Microbiol 2000, 37:467-476.
11. Kidgell C., Pickard D., Wain J., James K., Diem Nga L.T., Diep T.S., et al. Characterization and distribution of a cryptic Salmonella typhi plasmid pHCM2. Plasmid 2002, 47:159-171.
12. Dreher T.W. Viral tRNAs and tRNA-like structures. Wiley Interdiscip Rev RNA 2010, 1:402-414.
13. Bailly-Bechet M., Vergassola M., Rocha E. Causes for the intriguing presence of tRNAs in phages. Genome Res 2007, 17:1486-1495.
14. Antonenka U., Nölting C., Heesemann J., Rakin A. Horizontal transfer of Yersinia high-pathogenicity island by the conjugative RP4 attB target-presenting shuttle plasmid. Mol Microbiol 2005, 57:727-734.
15. Kim M., Kim S., Ryu S. Complete genome sequence of bacteriophage SSU5 specific for Salmonella enterica serovar Typhimurium rough strains. J Virol 2012, 86:10894.
16. Gao F., Zhang C.T. GC-Profile: a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences. Nucleic Acids Res 2006, 34:W686-W691.
17. Prentice M.B., James K.D., Parkhill J., Baker S.G., Stevens K., Simmonds M.N., et al. Yersinia pestis pFra shows biovar-specific differences and recent common ancestry with a Salmonella enterica serovar Typhi plasmid. J Bacteriol 2001, 183:2586-2594.
18. Antonenka U., Nölting C., Heesemann J., Rakin A. Independent acquisition of site-specific recombination factors by asn tRNA gene-targeting genomic islands. Int J Med Microbiol 2006, 296:341-352.
19. Wright M.S., Haft D.H., Harkins D.M., Perez F., Hujer K.M., Bajaksouzian S., et al. New insights into dissemination and variation of the health care-associated pathogen Acinetobacter baumannii from genomic analysis. MBio 2014, 5:e00963-13.
20. Garcillán-Barcia M.P., Francia M.V., de la Cruz F. The diversity of conjugative relaxases and its application in plasmid classification. FEMS Microbiol Rev 2009, 33:657-687.
21. Sorensen S.J., Bailey M., Hansen L.H., Kroer N., Wuertz S. Studying plasmid horizontal transfer in situ: a critical review. Nat Rev Microbiol 2005, 3:700-710.
22. Markowitz V.M., Mavromatis K., Ivanova N.N., Chen I.M., Chu K., Kyrpides N.C. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 2009, 25:2271-2278.
23. Guo F.B., Zhang C.T. ZCURVE_V: a new self-training system for recognizing protein-coding genes in viral and phage genomes. BMC Bioinformatics 2006, 7:9.
24. Lowe T.M., Eddy S.R. TRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997, 25:955-964.
25. Gao F., Zhang C.T. Ori-Finder: a web-based system for finding oriCs in unannotated bacterial genomes. BMC Bioinformatics 2008, 9:79.
26. Grant J.R., Stothard P. The CGView Server: a comparative genomics tool for circular genomes. Nucleic Acids Res 2008, 36:W181-W184.
27. Leekitcharoenphon P., Kaas R.S., Thomsen M.C.F., Friis C., Rasmussen S., Aarestrup F.M. SnpTree-a web-server to identify and construct SNP trees from whole genome sequence data. BMC Genomics 2012, 13:S6.